||Cycads are ancestral lineage but recent diversification within 12 Mya. Cycas is the only genus recognized in the family Cycadaceae, and divides into six sections. In this study, we use multilocus analyses to evaluate the nucleotide diversity, phylogenetic relationship, Bayesian clustering analysis, divergence time, and Dispersal-Vicariance model among 15 cycad taxa from four sections of Asiorientales, Panzhihuanses, Stangerioides, and Wadeanae. In total, 125 samples were sampled and 4 chloroplast DNA fragments, 24 nuclear DNA loci, and 425 AFLP loci were used for phylogenetic estimation.|
Genetic diversity of the continental species is higher than the island taxa. In the Bayesian clustering analysis, the best grouping numbers, respectively, is inferred as 2, 4, and 2 in plastid DNA, 24 nuclear DNA, and 425 AFLP loci, respectively, and the second fit number of grouping is inferred as 3 and 5 in plastid DNA and 425 AFLP loci, respectively. In addition, the second fit number of grouping based on AFLP loci is congruent with geographical distribution. Due to recent diversification, phylogenetic relationships revealed paraphyly or polyphyly within sections and may be resulting by incomplete lineage sorting. ASI group is composed of 2 species, C. revolute and C. taitungensis. TAG group contains the single species C. taiwaniana. PAN group contains the single species C. panzhihuaensis. STA group contains 9 species in section Stangerioides and one individual of C. taitungensis. CWG group contains the single species C. wadei. CUG group contains the single species C. curranii.
Using models of isolation with migration and BEAST sofeware to estimate the divergence time are not older than 6 Mya. The extant population sizes is extremely large (1.77×〖10〗^6~1.69×〖10〗^7), and the gene flows are asymmetry between groups. Current species distribution is affected by the oscillation of glaciation and the southwest China is the cycad biodiversity hotspot. Two migrate routes are start at the hotspot. The first migrate route is dispersal from southwest China to south China and Hainan Island. The second route is migrated from hotspot to southeast China and followed to Taiwan and Ryukyu Archipelago. The genetic components between taxa distributed on Hainan Island and mainland China are similar, but the genetic diversity for taxa distributed on Hainan Island is higher than other island taxa due to isolation from mainland China.